refloraR

refloraR is An R package for exploring plant specimen collections from REFLORA Virtual Herbarium hosted by Rio de Janeiro Botanical Garden. The package interacts with the REFLORA Integrated Publishing Toolkit (IPT) by readily downloading full specimen records for any herbarium in Darwin Core Format. Also, the package has specific functions to summarize information and filter specific information by taxonomic or geographical search.

The REFLORA programme

The study of Brazil’s flora, renowned as the richest in the world (BFG 2022), has a long and storied history. During the 18th and 19th centuries, European naturalists, along with a few Brazilian botanists, collected plant specimens while in Brazil, sending them to herbaria in Europe. The primary aim during this period was to investigate the flora and its potential uses. Many of these collections laid the groundwork for the description of new species or genera (serving as nomenclatural types), and were integral to the monumental work Flora brasiliensis (Martius, Eichler & Urban, 1840–1906), which described over 22,000 species.

In 2010, the Brazilian government launched the REFLORA/CNPq Programme, with the primary goal of retrieving and making accessible images and data related to Brazilian plant specimens stored primarily in overseas herbaria. These resources are now available through the REFLORA Virtual Herbarium. In 2014, this initiative was strengthened by the collaboration of SiBBr (Sistema de Informação sobre a Biodiversidade Brasileira) and the National Forest Inventory (IFN), which expanded the collections published under the Reflora project.

The REFLORA Virtual Herbarium platform was developed through a partnership between the Rio de Janeiro Botanical Garden (JBRJ) and COPPE (Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering, UFRJ). JBRJ hosts the system, overseeing the reception, storage, and publication of the herbarium images.

Complementing the REFLORA Virtual Herbarium is the Flora platform, first launched in 2008. This system has evolved through several stages—including the Lista de Espécies da Flora do Brasil, Flora do Brasil 2020, and now Flora e Funga do Brasil—and is also part of the broader REFLORA Programme. Flora e Funga do Brasil serves as a critical validator for the nomenclature of the REFLORA Virtual Herbarium’s images, which are continuously refined and enriched by taxonomists working collaboratively in an online system.

The REFLORA Programme has played a crucial role in Brazil’s success in meeting the goals of the Global Strategy for Plant Conservation, part of the Convention on Biological Diversity, for 2010 and 2020. As the challenges of understanding and studying biodiversity persist, the REFLORA systems will continue to provide unrestricted access to high-quality, accurate data on Brazil’s plants, algae, and fungi.

The REFLORA Virtual Herbarium

The mission to build a virtual herbarium to display the images of Brazilian plants housed in foreign herbaria was presented by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) to the Rio de Janeiro Botanical Garden (JBRJ) in December 2010. The objective was to provide the capacity to store and display high-quality data regarding Brazil’s Flora within a public institution. The Reflora Virtual Herbarium is designed to allow taxonomists to perform procedures similar to those they are accustomed to doing within physical collections. On this site, they have access to high-quality images rather than physical specimens, which can be consulted, re-determined, and typified, among other functionalities. Curators also have access to specimen determination reports to help update their physical collections. This innovative system has been available for study and update by a group of over 900 taxonomists involved in the List of Species of the Brazilian Flora and Brazilian Flora 2020 projects.

Initial partners of this initiative were the herbaria K (Royal Botanic Gardens, Kew), P (Muséum national d’histoire naturelle, Paris), and the RB (JBRJ) herbarium. From 2014 onwards, with the support of SiBBr (Sistema de Informação sobre a Biodiversidade Brasileira) and IFN (Inventário Florestal Nacional), other European, American, and Brazilian herbaria were included in this initiative, many of which received equipment and training to digitize their plant specimens.

Currently, 80 collections are published on the platform:

[**ACAM**](https://ipt.jbrj.gov.br/reflora/resource?r=acam) (Universidade Estadual da Paraíba), [**ALCB**](https://ipt.jbrj.gov.br/reflora/resource?r=alcb_herbarium) (Universidade Federal da Bahia), [**ASE**](https://ipt.jbrj.gov.br/reflora/resource?r=ase_herbarium) (Universidade Federal de Sergipe), [**B**](https://ipt.jbrj.gov.br/reflora/resource?r=b_herb) (Berlin Botanical Garden and Botanical Museum), [**BRBA**](https://ipt.jbrj.gov.br/reflora/resource?r=brba) (Universidade Federal do Oeste da Bahia), [**CEN**](https://ipt.jbrj.gov.br/reflora/resource?r=cen) ( Embrapa Recursos Genéticos e Biotecnologia), [**CEPEC**](https://ipt.jbrj.gov.br/reflora/resource?r=cepec_herbarium) (Centro de Pesquisas do Cacau), [**CESJ**](https://ipt.jbrj.gov.br/reflora/resource?r=cesj) (Universidade Federal de Juiz de Fora), [**CGMS**](https://ipt.jbrj.gov.br/reflora/resource?r=cgms) (Universidade Federal de Mato Grosso do Sul), [**COR**](https://ipt.jbrj.gov.br/reflora/resource?r=cor) (Universidade Federal de Mato Grosso do Sul), [**CRI**](https://ipt.jbrj.gov.br/reflora/resource?r=cri) (Universidade do Extremo Sul Catarinense), [**DVPR**](https://ipt.jbrj.gov.br/reflora/resource?r=dvpr) (Universidade Tecnológica Federal do Paraná), [**E**](https://ipt.jbrj.gov.br/reflora/resource?r=e_hv) (Royal Botanic Garden Edinburgh), [**EAC**](https://ipt.jbrj.gov.br/reflora/resource?r=eac_herbarium) (Universidade Federal do Ceará), [**EBC**](https://ipt.jbrj.gov.br/reflora/resource?r=ebc) (Economic Botany Collection), [**ECT**](https://ipt.jbrj.gov.br/reflora/resource?r=ect) (Embrapa Clima Temperado), [**ESA**](https://ipt.jbrj.gov.br/reflora/resource?r=esa_herbarium) (Universidade de São Paulo), [**EVB**](https://ipt.jbrj.gov.br/reflora/resource?r=evb) (Universidade Federal da Integração Latino-Americana), [**FLOR**](https://ipt.jbrj.gov.br/reflora/resource?r=flor_herbarium) (Universidade Federal de Santa Catarina), [**FURB**](https://ipt.jbrj.gov.br/reflora/resource?r=furb_herbarium) (Universidade Regional de Blumenau), [**GH**](https://ipt.jbrj.gov.br/reflora/resource?r=gh_herb) (Harvard University), [**HBR**](https://ipt.jbrj.gov.br/reflora/resource?r=hbr_herbarium) (Universidade Federal de Santa Catarina), [**HCF**](https://ipt.jbrj.gov.br/reflora/resource?r=hcf) (Universidade Tecnológica Federal do Paraná), [**HDCF**](https://ipt.jbrj.gov.br/reflora/resource?r=hdcf_herbarium) (Universidade Federal de Santa Maria), [**HEPH**](https://ipt.jbrj.gov.br/reflora/resource?r=heph) (Jardim Botânico de Brasília), [**HERBAM**](https://ipt.jbrj.gov.br/reflora/resource?r=herbam) (Universidade do Estado de Mato Grosso), [**HRCB**](https://ipt.jbrj.gov.br/reflora/resource?r=hrcb) (Universidade Estadual Paulista), [**HSTM**](https://ipt.jbrj.gov.br/reflora/resource?r=hstm) (Universidade Federal do Oeste do Pará), [**HTO**](https://ipt.jbrj.gov.br/reflora/resource?r=hto) (Universidade Federal do Tocantins), [**HUCP**](https://ipt.jbrj.gov.br/reflora/resource?r=hucp) (Pontífica Universidade Católica do Paraná), [**HUEFS**](https://ipt.jbrj.gov.br/reflora/resource?r=huefs) (Universidade Estadual de Feira de Santana), [**HUEM**](https://ipt.jbrj.gov.br/reflora/resource?r=huem) (Universidade Estadual de Maringá), [**HUEMG**](https://ipt.jbrj.gov.br/reflora/resource?r=huemg) (Universidade do Estado de Minas Gerais), [**HUENF**](https://ipt.jbrj.gov.br/reflora/resource?r=huenf) (Universidade Estadual do Norte Fluminense), [**HUFU**](https://ipt.jbrj.gov.br/reflora/resource?r=hufu_herbarium) (Universidade Federal de Uberlândia), [**HUNI**](https://ipt.jbrj.gov.br/reflora/resource?r=huni) (Universidade Federal do Estado do Rio de Janeiro), [**HURB**](https://ipt.jbrj.gov.br/reflora/resource?r=hurb) (Universidade do Recôncavo da Bahia), [**HVASF**](https://ipt.jbrj.gov.br/reflora/resource?r=hvasf) (Universidade Federal do Vale do São Francisco), [**HVAT**](https://ipt.jbrj.gov.br/reflora/resource?r=hvat) (Universidade do Vale do Taquari), [**IAN**](https://ipt.jbrj.gov.br/reflora/resource?r=ian) (Embrapa Amazônia Oriental), [**IBGE**](https://ipt.jbrj.gov.br/reflora/resource?r=ibge) (Herbário IBGE), [**ICN**](https://ipt.jbrj.gov.br/reflora/resource?r=icn) (Universidade Federal do Rio Grande do Sul), [**JOI**](https://ipt.jbrj.gov.br/reflora/resource?r=joi) (Universidade da Região de Joinville), [**K**](https://ipt.jbrj.gov.br/reflora/resource?r=k_reflora) (Royal Botanic Gardens, Kew), [**LUSC**](https://ipt.jbrj.gov.br/reflora/resource?r=lusc) (Universidade do Estado de Santa Catarina), [**MAC**](https://ipt.jbrj.gov.br/reflora/resource?r=mac) (Instituto do Meio Ambiente do Estado de Alagoas), [**MBM**](https://ipt.jbrj.gov.br/reflora/resource?r=mbm_herbarium) (Museu Botânico Municipal), [**MBML**](https://ipt.jbrj.gov.br/reflora/resource?r=mbml) (Museu de Biologia Mello Leitão), [**MG**](https://ipt.jbrj.gov.br/reflora/resource?r=mg_herbarium) (Museu Paraense Emílio Goeldi), [**MOH**](https://ipt.jbrj.gov.br/reflora/resource?r=moh) ( Missouri Botanical Garden), [**MUFAL**](https://ipt.jbrj.gov.br/reflora/resource?r=mufal) (Universidade Federal de Alagoas), [**NYH**](https://ipt.jbrj.gov.br/reflora/resource?r=nyh) (The New York Botanical Garden), [**P**](https://ipt.jbrj.gov.br/reflora/resource?r=p_reflora) (Muséum national d’Histoire naturelle), [**PC**](https://ipt.jbrj.gov.br/reflora/resource?r=pc_herb) (Cryptogamy Collection at the Muséum national d'Histoire naturelle), [**PEL**](https://ipt.jbrj.gov.br/reflora/resource?r=pel) (Universidade Federal de Pelotas), [**PMSP**](https://ipt.jbrj.gov.br/reflora/resource?r=pmsp) (Prefeitura do Município de São Paulo), [**R**](https://ipt.jbrj.gov.br/reflora/resource?r=r_herbarium) (Museu Nacional), [**RB**](https://ipt.jbrj.gov.br/reflora/resource?r=rb_herbarium) (Instituto de Pesquisas Jardim Botânico do Rio de Janeiro), [**RBR**](https://ipt.jbrj.gov.br/reflora/resource?r=rbr) (Universidade Federal Rural do Rio de Janeiro), [**REAL**](https://ipt.jbrj.gov.br/reflora/resource?r=real) (Universidade Federal da Fronteira Sul), [**RFA**](https://ipt.jbrj.gov.br/reflora/resource?r=rfa) (Universidade Federal do Rio de Janeiro), [**RFFP**](https://ipt.jbrj.gov.br/reflora/resource?r=rffp) (Universidade do Estado do Rio de Janeiro), [**RON**](https://ipt.jbrj.gov.br/reflora/resource?r=ron) (Universidade Federal de Rondônia), [**RSPF**](https://ipt.jbrj.gov.br/reflora/resource?r=rspf) (Universidade de Passo Fundo), [**S**](https://ipt.jbrj.gov.br/reflora/resource?r=s_reflora) (Naturhistoriska Riksmuseet), [**SAMES**](https://ipt.jbrj.gov.br/reflora/resource?r=sames) (Universidade Federal do Espírito Santo), [**SJRP**](https://ipt.jbrj.gov.br/reflora/resource?r=sjrp) (Universidade Estadual Paulista Júlio de Mesquita Filho), [**SLUI**](https://ipt.jbrj.gov.br/reflora/resource?r=slui) (Universidade Estadual do Maranhão), [**SOF**](https://ipt.jbrj.gov.br/reflora/resource?r=sof) (Swiss Orchid Foundation), [**SPF**](https://ipt.jbrj.gov.br/reflora/resource?r=spf_herbarium) (Universidade de são Paulo), [**TEPB**](https://ipt.jbrj.gov.br/reflora/resource?r=tepb) (Universidade Federal do Piauí), [**UB**](https://ipt.jbrj.gov.br/reflora/resource?r=ub_herbarium) (Universidade de Brasília), [**UFG**](https://ipt.jbrj.gov.br/reflora/resource?r=ufg) (Universidade Federal de Goiás), [**UFRN**](https://ipt.jbrj.gov.br/reflora/resource?r=ufrn) (Universidade Federal do Rio Grande do Norte), [**UNIP**](https://ipt.jbrj.gov.br/reflora/resource?r=unip) (Universidade Paulista), [**UNOP**](https://ipt.jbrj.gov.br/reflora/resource?r=unop) (Universidade Estadual do Oeste do Paraná), [**UPCB**](https://ipt.jbrj.gov.br/reflora/resource?r=upcb_herbarium) (Universidade Federal de Paraná), [**US**](https://ipt.jbrj.gov.br/reflora/resource?r=us_reflora) (Smithsonian Institution), [**VIES**](https://ipt.jbrj.gov.br/reflora/resource?r=vies_herbarium) (Universidade Federal do Espírito Santo), [**W**](https://ipt.jbrj.gov.br/reflora/resource?r=w_reflora) (Naturhistorisches Museum Wien).

There are now 4,602,397 images of specimens available in the REFLORA Virtual Herbarium. Among them, 157,652 are nomenclatural types and 1,985,843 are georeferenced records.

If you are an herbarium curator and wish to publish images and data from your collection in REFLORA Virtual Herbarium, send a request to the contact email reflora@jbrj.gov.br.

:::

Get Started

Welcome new users! Start here to learn how to install and use refloraR.

Articles

“How-to” articles to help you learn how to interact with refloraR.

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---
format:
  html:
    toc: true
    page-layout: custom
execute:
  echo: false
  eval: true
  freeze: auto
  cache: false
  warning: false
  message: false
  include: true
  # ENABLE inline R code evaluation
  inline: true
---

```{r setup, include=FALSE}
library(refloraR)

summary_df <- reflora_summary(verbose = FALSE,
                              save = FALSE,
                              dir = "reflora_summary")
```

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\
\
***refloraR*** is An R package for exploring plant specimen collections from [REFLORA Virtual Herbarium](https://ipt.jbrj.gov.br/reflora) hosted by [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj). The package interacts with the REFLORA Integrated Publishing Toolkit (IPT) by readily downloading full specimen records for any herbarium in Darwin Core Format. Also, the package has specific functions to summarize information and filter specific information by taxonomic or geographical search.\
\

## The REFLORA programme

The study of Brazil's flora, renowned as the richest in the world ([BFG 2022](https://doi.org/10.1002/tax.12640)), has a long and storied history. During the 18th and 19th centuries, European naturalists, along with a few Brazilian botanists, collected plant specimens while in Brazil, sending them to herbaria in Europe. The primary aim during this period was to investigate the flora and its potential uses. Many of these collections laid the groundwork for the description of new species or genera (serving as nomenclatural types), and were integral to the monumental work Flora brasiliensis ([Martius, Eichler & Urban, 1840–1906](https://www.biodiversitylibrary.org/bibliography/454)), which described over 22,000 species.

In 2010, the Brazilian government launched the REFLORA/CNPq Programme, with the primary goal of retrieving and making accessible images and data related to Brazilian plant specimens stored primarily in overseas herbaria. These resources are now available through the REFLORA Virtual Herbarium. In 2014, this initiative was strengthened by the collaboration of SiBBr (Sistema de Informação sobre a Biodiversidade Brasileira) and the National Forest Inventory (IFN), which expanded the collections published under the Reflora project.

The [REFLORA Virtual Herbarium](https://floradobrasil.jbrj.gov.br/reflora/herbarioVirtual/ConsultaPublicoHVUC/ConsultaPublicoHVUC.do) platform was developed through a partnership between the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj) and [COPPE (Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering, UFRJ)](https://coppe.ufrj.br/en/home-en/). JBRJ hosts the system, overseeing the reception, storage, and publication of the herbarium images.

Complementing the REFLORA Virtual Herbarium is the Flora platform, first launched in 2008. This system has evolved through several stages—including the Lista de Espécies da Flora do Brasil, [Flora do Brasil 2020](http://doi.org/10.47871/jbrj2021004), and now [Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/)—and is also part of the broader REFLORA Programme. Flora e Funga do Brasil serves as a critical validator for the nomenclature of the REFLORA Virtual Herbarium’s images, which are continuously refined and enriched by taxonomists working collaboratively in an online system.

The REFLORA Programme has played a crucial role in Brazil’s success in meeting the goals of the Global Strategy for Plant Conservation, part of the Convention on Biological Diversity, for 2010 and 2020. As the challenges of understanding and studying biodiversity persist, the REFLORA systems will continue to provide unrestricted access to high-quality, accurate data on Brazil's plants, algae, and fungi.\
\

## The REFLORA Virtual Herbarium

The mission to build a virtual herbarium to display the images of Brazilian plants housed in foreign herbaria was presented by the [Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)](https://www.gov.br/cnpq/pt-br) to the Rio de Janeiro Botanical Garden (JBRJ) in December 2010. The objective was to provide the capacity to store and display high-quality data regarding Brazil’s Flora within a public institution. The Reflora Virtual Herbarium is designed to allow taxonomists to perform procedures similar to those they are accustomed to doing within physical collections. On this site, they have access to high-quality images rather than physical specimens, which can be consulted, re-determined, and typified, among other functionalities. Curators also have access to specimen determination reports to help update their physical collections. This innovative system has been available for study and update by a group of over 900 taxonomists involved in the List of Species of the Brazilian Flora and Brazilian Flora 2020 projects.

Initial partners of this initiative were the herbaria [**K**](https://www.kew.org) (Royal Botanic Gardens, Kew), [**P**](https://www.mnhn.fr/fr/collection-des-plantes-vasculaires) (Muséum national d’histoire naturelle, Paris), and the [**RB**](https://www.gov.br/jbrj) (JBRJ) herbarium. From 2014 onwards, with the support of [**SiBBr**](https://www.sibbr.gov.br) (Sistema de Informação sobre a Biodiversidade Brasileira) and [**IFN**](https://www.gov.br/florestal/pt-br/assuntos/ifn) (Inventário Florestal Nacional), other European, American, and Brazilian herbaria were included in this initiative, many of which received equipment and training to digitize their plant specimens.

Currently, **`r length(summary_df$collectionCode)`** collections are published on the platform:

```{r}
#| echo: false
for (i in seq_along(summary_df$collectionCode)) {
  if (i < length(summary_df$collectionCode)) {
  cat(paste0("[**", summary_df$collectionCode[i], "**]", "(", summary_df$Reflora_URL[i], ")"), paste0("(", summary_df$rightsHolder[i], "), "))
  } else {
    cat(paste0("[**", summary_df$collectionCode[i], "**]", "(", summary_df$Reflora_URL[i], ")"), paste0("(", summary_df$rightsHolder[i], ")."))
  }
}
```

There are now 4,602,397 images of specimens available in the REFLORA Virtual Herbarium. Among them, 157,652 are nomenclatural types and 1,985,843 are georeferenced records.

If you are an herbarium curator and wish to publish images and data from your collection in REFLORA Virtual Herbarium, send a request to the contact email **reflora\@jbrj.gov.br**.\
\
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![](figures/refloraR_hex_sticker.png){style="align: right;" width="200"}

![](figures/JBRJ-Marca_Vt-VK-S-P-B_v01.jpg){style="align: right;" width="200"}
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### [Get Started](/get-started/index.qmd)

**Welcome new users!** Start here to learn how to install and use ***refloraR***.
:::

::: {style="text-align: center;"}
### [Articles](/articles/index.qmd)

"How-to" articles to help you learn how to interact with ***refloraR***.
:::
:::
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